Forward-Looking Statements

The following discussion and analysis should be read together with our consolidated financial statements and the notes to those statements included elsewhere in this Form 10-Q. This Form 10-Q contains forward-looking statements within the meaning of Section 27A of the Securities Act of 1933, as amended (Securities Act), and Section 21E of the Securities Exchange Act of 1934, as amended, or the Exchange Act, that are based on our management's beliefs and assumptions and on information currently available to our management. The forward-looking statements are contained principally in the section entitled "Risk Factors" and this Management's Discussion and Analysis of Financial Condition and Results of Operations. Forward-looking statements include, but are not limited to:



    •   the sufficiency of our cash and cash equivalents and cash generated from
        operations to meet our working capital and capital expenditure needs for
        the next 12 months;


    •   the performance of our collaboration partner Alvogen, upon which we are
        dependent on to commercialize the FDA-approved PF708 product;


    •   our reliance on Jazz Pharmaceuticals Ireland Ltd. (Jazz), Alvogen Malta
        Operations Ltd. (Alvogen), China NT Pharma Group Company Ltd. (NT Pharma),
        Merck & Co., Inc. (Merck), Serum Institute of India Private Ltd. (SIIPL)
        and any future collaboration partner's performance over which we do not
        have control;


    •   our expectations regarding the potential impacts on our business, access
        to capital, supply chain, preclinical programs and clinical trials of the
        novel coronavirus (COVID-19) pandemic;


    •   our and any potential future collaboration partner's ability to enroll
        patients in our clinical studies at the pace that we project;


  • our expectation to expand our product pipeline;


    •   our expectations regarding the initiation, timing, progress and the
        success of the design, primary and secondary end points, and duration of
        the clinical trials and planned clinical trials and studies for our
        current product candidates and reporting results from same;


    •   whether the results of our and our collaboration partners' trials and
        studies will be sufficient to support domestic or global regulatory
        filings and approvals for PF708, and whether and when we are able to
        obtain an "A" therapeutic equivalence designation for the FDA-approved
        PF708 product relative to the reference drug Forteo;


    •   our and our collaboration partners' ability to maintain regulatory
        approval of the FDA-approved PF708 product or seek and obtain regulatory
        approval for PF708 and our other product candidates, and if approved,
        maintain regulatory approval and the timing of such potential regulatory
        approvals;


    •   our expectations with respect to the commercialization of the FDA-approved
        PF708 product by Alvogen;


  • our reliance on third-parties to conduct clinical studies;


    •   our reliance on third-party contract manufacturers and Alvogen to
        manufacture and supply the FDA-approved PF708 product, PF708 and our other
        product candidates for us;


    •   the benefits of the use of the FDA-approved PF708 product, PF708, or any
        of our other product candidates;


    •   the rate and degree of market acceptance of the FDA-approved PF708
        product, PF708 or any of our other product candidates, if approved for
        sale;


  • regulatory developments in the United States and foreign countries;


    •   our expectations regarding government and third-party payor coverage and
        reimbursement;


    •   our and our collaboration partners' ability to manufacture the
        FDA-approved PF708 product, PF708 and our other product candidates in
        conformity with regulatory requirements and to scale up manufacturing of
        the FDA-approved PF708 product, PF708 and our other product candidates to
        commercial scale;


    •   our ability to successfully build a specialty sales force, or collaborate
        with third-parties including our existing collaboration partners, Alvogen
        and NT Pharma, to commercialize the FDA-approved PF708 product, PF708 and
        our other product candidates;


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    •   our and our collaboration partners' ability to compete with companies
        currently producing the reference products, including Forteo;


    •   our ability to compete with companies that may also seek and obtain
        approval for therapeutically equivalent versions of Forteo;


    •   our ability to retain and recruit key personnel, including development of
        a sales and marketing function;


    •   our ability to obtain and maintain intellectual property protection for
        the FDA-approved PF708 product, PF708, our Pf?nex Expression Technology®
        or any other product candidates;


    •   our estimates of our expenses, ongoing losses, future revenue, capital
        requirements and our needs for or ability to obtain additional financing;


    •   our expectations regarding the market size, size of patient populations,
        and growth potential for the FDA-approved PF708 product, PF708 and our
        product candidates, if approved for commercial use;


    •   our estimates of the expected patent expiration timelines for Forteo and
        other branded reference drugs and biologics;


  • our ability to develop new products and product candidates;


    •   our ability to successfully establish and successfully maintain
        appropriate collaborations and derive significant revenue from those
        collaborations;


  • our financial performance; and


  • developments and projections relating to our competitors and our industry.



Forward-looking statements include statements that are not historical facts and can be identified by terms such as "anticipates," "believes," "could," "seeks," "estimates," "expects," "intends," "may," "plans," "potential," "predicts," "projects," "should," "will," "would," or similar expressions and the negatives of those terms. Forward-looking statements involve known and unknown risks, uncertainties, and other factors that may cause our actual results, performance, or achievements to be materially different from any future results, performance, or achievements expressed or implied by the forward-looking statements. We discuss these risks in greater detail in Part II, Item 1A, "Risk Factors," elsewhere in this Form 10-Q filed with the Securities and Exchange Commission, or SEC. Given these uncertainties, you should not place undue reliance on these forward-looking statements. Also, forward-looking statements represent our management's beliefs and assumptions only as of the date of this Form 10-Q. In addition, statements that "we believe" and similar statements reflect our beliefs and opinions on the relevant subject. These statements are based upon information available to us as of the date of this Form 10-Q, and although we believe such information forms a reasonable basis for such statements, such information may be limited or incomplete, and our statements should not be read to indicate that we have conducted a thorough inquiry into, or review of, all potentially available relevant information. These statements are inherently uncertain and investors are cautioned not to unduly rely upon these statements.

Except as required by law, we assume no obligation to update these forward-looking statements, or to update the reasons actual results could differ materially from those anticipated in these forward-looking statements, even if new information becomes available in the future. You should read this Form 10-Q completely and with the understanding that our actual future results may be materially different from what we expect.

This Quarterly Report on Form 10-Q also contains estimates, projections and other information concerning our industry, our business, and the markets for certain diseases, including data regarding the estimated size of those markets. Information that is based on estimates, forecasts, projections, market research or similar methodologies is inherently subject to uncertainties and actual events or circumstances may differ materially from events and circumstances reflected in this information. Unless otherwise expressly stated, we obtained this industry, business, market, and other data from reports, research surveys, studies, and similar data prepared by market research firms and other third parties, industry, medical and general publications, government data, and similar sources.

Pf?nexTM, Pfenex Biopharmaceuticals™, the Pfenex Biopharmaceuticals logo, and Pf?nex Expression Technology® are among our primary trademarks. Other trademarks referred to in this Form 10-Q are the property of their respective owners.

In this Form 10-Q, "we," "us" and "our" refer to Pfenex Inc. and its subsidiaries.



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Overview

We are a development and licensing biotechnology company focused on leveraging our proprietary protein production platform, Pf?nex Expression Technology®, to develop next generation and novel protein therapeutics to meaningfully improve existing therapies and create novel therapies for some of the biological targets linked to critical diseases still waiting to successfully be addressed. We have extensive experience in protein therapeutic development and our proven platform enables deliberate and rapid candidate selection, fast drug development, and potentially higher success rates for a wide range of complex modalities. We aim to leverage existing drug development successes into a broad pipeline that is diversified across multiple assets, including an FDA-approved product and next generation and novel biopharmaceutical product candidates.

In October 2019, the FDA approved the new drug application (NDA) for PF708 under the 505(b)(2) regulatory pathway, with Forteo® (teriparatide injection) as the reference drug. The FDA-approved PF708 product is indicated for the treatment of osteoporosis in certain patients at high risk for fracture. Marketing authorization applications are pending in other jurisdictions. This FDA-approved PF708 product will be commercialized and manufactured in the U.S. by our collaboration partner, Alvogen Malta Operations Ltd. (Alvogen). In November 2019, in accordance with the Development and License Agreement (US Alvogen Agreement), we transferred the NDA to Alvogen. Alvogen is currently evaluating a potential U.S. commercial launch upon or before an FDA decision on therapeutic equivalence. We expect to continue to support Alvogen with its commercial strategy planning in the U.S. while continuing to seek "A" therapeutic equivalence designation.

Our other product candidates and collaborations include PF743 (JZP-458), which we are developing in collaboration with Jazz Pharmaceuticals for the treatment of acute lymphoblastic leukemia (ALL) or lymphoblastic lymphoma and which commenced a pivotal Phase 2/3 clinical study in December 2019. We also have collaborations based on CRM197, a diphtheria toxoid carrier protein used in prophylactic and therapeutic vaccine candidates, with Merck & Co., Inc. (Merck) and Serum Institute of India Private Limited (SIIPL). Both Merck and SIIPL have licenses to the Pf?nex Expression Technology for the production of CRM197 for use in conjugate vaccine products. Merck's V114, a 15-valent Pneumococcal conjugate vaccine is currently in 15 Phase 3 clinical trials, and SIIPL's Pneumosil®, a 10-valent Pneumococcal vaccine designed for the developing world, recently achieved World Health Organization (WHO) Prequalification allowing the product to be procured by United Nations agencies and Gavi, the Vaccine Alliance. In addition, a Phase 3, randomized, double-blind study to evaluate the immunogenicity, safety and tolerability of Pneumosil in healthy Indian infants has been completed and SIIPL is currently in the process of submitting the data from the Phase 3 trial to the Drug Controller General of India (DCGI) in support of India marketing authorization.

In the third quarter of 2019, we added PF810, a peptide based next generation therapeutic, to our wholly owned pipeline. PF810 is currently in preclinical development. In addition, we have established a strategic collaboration with Arcellx, Inc. (Arcellx) to advance multiple proprietary sparX proteins that activate, silence and reprogram Antigen-Receptor Complex T cell based therapies based on the Arcellx product platform.





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Our FDA-Approved Product, Our Product Candidates and Collaborations

The following summarizes certain information about the FDA-approved product that we developed, our pipeline candidates, and collaborations:





Our FDA-Approved Product,
Product Candidates and             Branded
Collaborations                  Reference Drug                 Program
FDA-Approved PF708 Product         Forteo®        • Approved in the United States;
                                                  licensed to Alvogen

PF708                              Forteo®        • Product candidate in EU, MENA,
                                                  and Rest of World licensed to
                                                  Alvogen (excluding areas licensed
                                                  to NT Pharma)
                                                  • Product candidate in Mainland
                                                  China, Hong Kong, Singapore,
                                                  Malaysia, Thailand licensed to NT
                                                  Pharma

Hematologic Oncology Product         N/A          • PF743 (JZP-458) - Recombinant
Candidates                                        Erwinia asparaginase
                                                  • PF745 (JZP-341) - Long-acting
                                                  recombinant Erwinia asparaginase
                                                  • PF690* - pegaspargase

Peptide based next                   N/A          • PF810
generation therapeutic

Arcellx sparX programs               N/A          • PF753
                                                  • PF754
                             ­




*Jazz retains an exclusive option to license this product pursuant to certain option triggers.

In pursuit of novel wholly-owned product candidates, we have also established a collaboration with a third-party technology platform company that is screening our selected, validated biological targets with its novel binding modality library in an effort to identify potential lead product candidates. Those candidates will be transferred to us and could become wholly owned product candidates developed by us.



FDA-Approved PF708 Product



In October 2019, the FDA approved the NDA for PF708 under the 505(b)(2) regulatory pathway, with Forteo® (teriparatide injection) as the reference drug. The FDA-approved PF708 product is indicated for the treatment of osteoporosis in certain patients at high risk for fracture. The FDA-approved PF708 product will be commercialized and manufactured in the U.S. by our collaboration partner, Alvogen. In November 2019, we transferred the NDA to Alvogen pursuant to our collaboration agreement. Forteo (marketed by Eli Lilly and Company) achieved $1.4 billion in global product sales in 2019. Almost half of these product sales came from the United States alone. We expect to continue to support Alvogen with its commercial strategy planning in the U.S. while continuing to seek "A" therapeutic equivalence designation.

The FDA approval of the FDA-approved PF708 product was supported by data from Study PF708-301, which compared the effect of PF708 and Forteo in osteoporosis patients. The PF708-301 study enrolled a total of 181 patients, with 90 patients receiving PF708 and 91 patients receiving Forteo. Eighty-two patients completed the study in the FDA-approved PF708 product treatment group, compared with 81 patients in the Forteo treatment group. The primary study endpoint was anti-drug antibody (ADA) incidence after 24 weeks of drug treatment. 2.2% (2/90) of patients who received PF708 and 2.2% (2/91) of patients who received Forteo had detectable antibodies to teriparatide, and one of the two patients who received PF708 developed neutralizing antibodies to teriparatide. The secondary study endpoints included mean percentage changes in lumbar-spine bone mineral density (BMD) and median percentage changes in bone turnover markers (BTM) after 24 weeks of drug treatment, as well as pharmacokinetic (PK) parameters for up to four hours after the first dose. Safety endpoints were incidences of adverse events (AE) and serious adverse events (SAE).





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The PF708-301 study showed comparable overall profiles between PF708 and Forteo across multiple endpoints. These results from the PF708-301 study, along with bioequivalence findings from Study PF708-101 in healthy subjects, supported the PF708 NDA submitted in December 2018 pursuant to the 505(b)(2) pathway. On October 4, 2019 the NDA was approved by the FDA.

In addition to obtaining FDA approval of PF708, we have been continuing our efforts to obtain an "A" therapeutic equivalence designation for the product relative to its reference drug, Forteo. A determination of therapeutic equivalence (as shown by an "A" rating) may permit the FDA-approved PF708 product to be automatically substituted for Forteo, depending on applicable laws and policies within each of the 50 states in the U.S. Consistent with our interactions with the FDA and the agency's draft guidance document on comparative use human factors studies for demonstrating the therapeutic equivalence of drug-device combination products, we successfully completed a PF708 comparative use human factors (HF) study and submitted the final study report to the FDA in October 2019.

The comparative use HF study was a simulated use study intended to evaluate the effect of each product's delivery device and user interface on critical task performance by untrained osteoporosis patients and caregivers. The study used a paired design of the FDA-approved PF708 and the Forteo products and included both naïve and Forteo experienced users. On April 9, 2020, the FDA informed Alvogen that additional comparative use human factors data, specifically from additional Forteo experienced users, would be required before the agency could make a determination about therapeutic equivalence. FDA has indicated that the review of the PF708 therapeutic equivalence package continues and provided guidance on study methodology to generate this additional comparative use human factors data. We plan to work closely with Alvogen and the FDA to generate and submit these additional data as soon as possible.

For a discussion of certain significant risks relating to the FDA-approved PF708 product, please see the following Risk Factors: "The FDA-approved PF708 product, PF708 and our other product candidates, if approved, face significant competition from the reference products and from therapeutic equivalent products of the reference products, and from other products. Our or our collaboration partners' failure to effectively compete may prevent us from achieving significant market penetration and expansion." and "If the FDA-approved PF708 product does not receive an "A" therapeutic equivalence designation from the FDA, our business may suffer."

In June 2018, we and Alvogen entered into the US Alvogen Agreement pursuant to which Alvogen received the exclusive right to commercialize and manufacture PF708 in the United States. We expect to continue to support Alvogen with its commercial strategy planning in the U.S. while continuing to seek "A" therapeutic equivalence designation. In February 2019, we and Alvogen expanded our collaboration, granting Alvogen exclusive rights to commercialize and manufacture PF708, upon receipt of applicable marketing authorizations, in the EU, certain countries in the Middle East and North Africa (MENA), and the rest of the world (ROW) territories (the latter defined as all countries outside of the EU, US and MENA, excluding Mainland China, Hong Kong, Singapore, Malaysia and Thailand). We believe this collaboration leverages Alvogen's established international experience and expertise in regulatory, IP and supply chain activities, as well as its established network of specialty pharmaceutical companies to conduct sales and marketing activities in these regions.

Alvogen submitted a centralized application to the European Medicines Agency (EMA) for PF708 on May 6, 2019, and the filing was accepted by the EMA on May 23, 2019. We believe that PF708 could be approved in the EU as early as the second half of 2020, pending marketing authorization by the European Commission under the EU centralized procedure and other factors. In October 2019, Alvogen's partner SAJA, submitted a Marketing Authorization Application (MAA) for PF708 to the Kingdom of Saudi Arabia's Saudi Food and Drug Authority (SFDA). Subject to applicable regulatory approvals, PF708 will be commercialized in Europe and other jurisdictions by Alvogen's current and/or future commercialization partners including Theramex in Europe, SAJA, a Tamer Group company in MENA, JAMP Pharma in Canada, Kamada Ltd. in Israel, Pharmbio Korea, Inc. in South Korea and Juno Pharmaceuticals Pty Ltd in Australia and New Zealand. Alvogen is responsible for overseeing any clinical development, regulatory, litigation, commercial manufacturing or commercialization activities of its partners in these jurisdictions. We are eligible to receive additional upfront and milestone payments of $1.5 million for the EU, MENA and ROW agreements, and we may also be eligible to receive up to 60% of Alvogen's gross profit derived from product sales, if approved, depending on geography and cost of goods sold. In connection with the October 2019 FDA approval of PF708, we earned a $2.5 million milestone payment under our collaboration with Alvogen payable upon Alvogen's receipt of notice of NDA approval.

In April 2018, we and NT Pharma entered into a Development and License Agreement (NT Pharma Agreement), pursuant to which we granted an exclusive license to NT Pharma to commercialize PF708 in Mainland China, Hong Kong, Singapore, Malaysia and Thailand and a non-exclusive license to conduct development activities in such territories with respect to PF708. In accordance with the agreement, we received a payment of $2.5 million upon signing the NT Pharma Agreement and may be eligible to receive additional payments of up to $22.5 million based on the achievement of certain development, regulatory, and sales-related milestones.



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We may also be eligible to receive double-digit royalties on net sales of PF708. NT Pharma is responsible for any further development required to achieve regulatory approval as well as commercialization activities in the applicable territories.

In accordance with regulatory requirements we provided notice of Paragraph IV certification (Notice Letter) to Eli Lilly and Company (Lilly) on February 19, 2019 that PF708 does not infringe any valid claim of the '334 patent. Under the Hatch-Waxman Act, Lilly had 45 days from the receipt of the Notice Letter to file a patent infringement lawsuit against us that would cause a 30-month litigation stay of approval for PF708. On April 11, 2019 we announced the expiration of the 45-day period for Lilly to file a lawsuit under the Hatch-Waxman Act and stay the approval of PF708 for 30 months. Lilly did not file a lawsuit within this time period, and there was no 30-month litigation stay that delayed approval of the FDA-approved PF708 product.

In May 2019, we entered into an agreement with Alvogen for us to provide PF708 drug substance batches and pen components in exchange for $2.3 million. This product sold to Alvogen was initially manufactured by our CMO for manufacturing process validation purposes as part of the PF708 NDA submission to the FDA for approval. We do not expect to have similar transactions with our collaboration partners in the future.

Effective April 21, 2020, we entered into a Deed of Assignment and Amendment (Deed) with NT Pharma, NT Pharma International Company Limited (NT International), and Kangchen, a wholly-owned subsidiary of Konruns. Pursuant to the Deed, we agreed to allow NT Pharma to assign its rights and obligations under the NT Pharma Agreement with the Company to Kangchen. Accordingly, all of NT Pharma's rights under the NT Pharma Agreement will be assigned to Kangchen, and Kangchen will assume all of NT Pharma's obligations under the NT Pharma Agreement. In a related transaction, NT Pharma, through NT International, will obtain an equity interest in Kangchen and each of NT Pharma and Konruns, as the ultimate parents of Kangchen, will jointly and severally guarantee for the benefit of Pfenex the obligations of Kangchen under the NT Pharma Agreement.

Jazz Collaboration - multiple hematologic oncology product candidates - In July 2016, we entered into a license and option agreement with Jazz, pursuant to which we and Jazz are developing hematologic oncology products, including PF743 (JZP-458), a recombinant Erwinia asparaginase, and PF745 (JZP-341), a long-acting recombinant Erwinia asparaginase, and Jazz will have the exclusive right to manufacture and commercialize such products throughout the world. In addition, pursuant to the agreement, we have granted Jazz certain other rights to negotiate the exclusive right to develop, manufacture and commercialize throughout the world other hematologic oncology products that are currently being, or in the future may be, developed by us. Both PF743 (JZP-458) and PF745 (JZP-341) are being developed for the treatment of ALL and other hematological malignancies. In the third quarter of 2017, we achieved a process development milestone associated with this collaboration. In December 2017, we and Jazz signed an amended and restated agreement under which we will be eligible to receive an additional $43.5 million in amendment fee and development milestone payments as compared to the 2016 agreement, increasing the total value of upfront, option and amendment fee payments and potential payments for the achievement of development, regulatory and sales-related milestones associated with the collaboration to an aggregate of $224.5 million. We will also continue to be eligible to receive tiered royalties on worldwide sales of any products resulting from the collaboration at rates reduced from those under the 2016 agreement. In December 2017, as part of the amended and restated agreement, we received a total payment of $18.5 million, consisting of an upfront payment of $5.0 million and a payment of $13.5 million for development achievement. In the second quarter of 2018, we achieved two development milestones and received $0.8 million for successful achievement of process development milestones for PF745. In August 2019, Jazz reported that they completed a Phase 1 study for PF743 (JZP-458). After receiving Fast Track designation from the U.S. Food and Drug Administration in October 2019, Jazz announced the initiation of a Phase 2/3 pivotal study for PF743(JZP-458) in December 2019 and recently announced their intent to file a Biologics License Application (BLA) with the US FDA as early as the fourth quarter of 2020. In September and December 2019, we achieved development milestones and received $11 million and $15 million, respectively, in connection with process development activities for PF745 (JZP-341).

CRM197 - We have both licenses and supply agreements in place for CRM197, which is a non-toxic mutant of diphtheria toxin. CRM197 is a well-characterized protein and functions as a carrier for polysaccharides and haptens, making them immunogenic. We have developed unique CRM197 production strains based on our Pf?nex Expression Technology platform. As a result of our development efforts, we previously entered into commercial licenses for production strains capable of producing CRM197 with both Merck and SIIPL. Merck and SIIPL are using the CRM197 produced via the licensed production strain in multiple clinical stage and pre-clinical product candidates. The clinical stage product candidates include Merck's 15-valent pneumococcal conjugate vaccine, PCV-15 (V114), currently in several ongoing Phase 3 clinical studies, and SIIPL's 10-valent pneumococcal conjugate vaccine, Pneumosil®, which achieved WHO Prequalification in December 2019, and a pentavalent meningococcal conjugate vaccine currently in a Phase 3 clinical study. The CRM197 production strains utilized by both Merck and SIIPL are unique and exclusively licensed to each party. The commercial license agreements with Merck and SIIPL contemplate potential maintenance and milestone fees as well as royalties on net sales. Additionally, as part of the SIIPL commercial license agreement, SIIPL supplies both reagent grade and cGMP CRM197 to Pfenex, which supplies the product to vaccine development-focused pharmaceutical partners.



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Arcellx Development, Evaluation and License Agreement - We previously entered into a development, evaluation and license agreement with Arcellx which provides access to the Pf?nex Expression Technology platform to advance Arcellx's proprietary sparX proteins that activate, silence and reprogram Antigen- Receptor Complex T cell-based therapies. Under the terms of the agreement, we are eligible to receive development funding in addition to development, regulatory and commercial milestones ranging from $2.6 million to $18 million for each product incorporating a sparX protein expressed using a production strain based on the Pf?nex Expression Technology, as well as royalties on worldwide sales of any such products. We have completed the development of both sparX 1 (PF753) and sparX 2 (PF754) and Arcellx has opted into the commercial license for both production strains. As of March 31, 2020, we have earned $2.4 million in development funding from Arcellx. During the three months ended March 31, 2020, there was no revenue recognized related to the Arcellx agreement.

Additional Biosimilar, Novel Vaccine and Other Pipeline Product Candidates - Our pipeline includes biosimilar candidates to certain reference products, including biosimilar candidates to Lucentis (PF582) and Neulasta (PF529) and two novel anthrax vaccine candidates, Px563L and RPA563, which are funded by the Biomedical Advanced Research and Development Authority (BARDA). In November of 2017, we paused development on both PF582 and PF529. We do not intend to advance PF582 or PF529 without development and commercial collaboration partners. In March 2019 we received a notice from BARDA advising us of BARDA's decision not to exercise development options for cGMP manufacturing, preclinical studies and Phase 1/2b study readiness in connection with our Px563L and RPA563 novel anthrax vaccine program. Following the receipt of the notice from BARDA and pursuant to discussions with BARDA, we deprioritized this program in our portfolio.

To date, PF708 is our only FDA approved product under the 505(b)(2) regulatory pathway, with Forteo as the reference drug. Our product candidates are enabled by our patented protein production platform, Pf?nex Expression Technology, which we believe confers several important competitive advantages compared to traditional techniques for protein production, including the ability to produce complex proteins with higher accuracy and greater degree of protein purity, as well as speed and cost advantages. The development of proteins requires several competencies which represent both challenges and barriers to entry. Due to their inherent complexity, proteins require the use of living organisms to efficiently produce them at a large scale. Traditional techniques for protein production employ a trial and error approach to production organism, or strain, selection and process optimization, which is inherently inefficient and typically produces suboptimal results. This historically inefficient process provides barriers to creating or replicating complex proteins, adds significant time to market and results in the high cost of goods typical of biologic therapeutics. Together, these limitations pose significant hurdles for companies interested in entering the market with novel biologics, biosimilars and therapeutic equivalents. Our platform utilizes a proprietary high throughput fully automated parallel approach, which allows the construction and testing of thousands of unique protein production strains in parallel, thereby allowing us to produce and characterize complex proteins while reducing the time and cost of development and long-term production.

The potential market opportunities for our most advanced product candidate, PF708, are substantial. We have developed PF708 as a therapeutic equivalent candidate to Forteo, which achieved global product sales of approximately $1.4 billion in 2019. Approximately 46% of these product sales came from the U.S. alone.

Our revenue for the three months ended March 31, 2020 and 2019 was $0.7 million and $7.9 million, respectively. Our historical revenue has been primarily derived from monetizing our Pf?nex Expression Technology through collaboration agreements, service agreements, government contracts and reagent protein product sales, which provide for various types of payments, including upfront payments, funding of research and development, milestone payments, intellectual property access fees and licensing fees.

As of March 31, 2020, we had an accumulated deficit of $207.9 million, of which $89.8 million was attributable to recognizing the accretion in the redemption value of our convertible preferred stock. We recognized net losses of $10.2 million and $6.1 million for the three months ended March 31, 2020 and 2019, respectively.

As we continue to develop and invest more resources into the development and commercialization of our product candidates, our net operating losses may increase over the next several years. Research and development expenses will continue to be material as we incur further costs of development. We are currently developing our wholly owned therapeutics, establishing additional product development partnerships, and investigating and targeting novel modalities for possible future lead candidates, and we do not yet have an extensive sales organization. We will need substantial additional funding to support our operating activities, especially as we approach anticipated regulatory approval in the United States, Europe and other territories, and begin to establish our commercialization capabilities. Adequate funding may not be available to us on commercially reasonable terms, or at all. Since our inception, we have funded our operations primarily through the sale and issuance of common stock in our public offerings, revenue from our collaboration agreements, government contracts, service agreements, and reagent protein product sales, our prior credit facility and the private placement of equity securities. We have devoted substantially all of our capital resources to the research and development of our product candidates and working capital requirements.



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Recent Developments

COVID-19 Pandemic

The novel coronavirus outbreak of COVID-19 has had and likely will continue to have significant effects on businesses and health care institutions around the world. While it is not possible at this time to estimate the overall impact that the COVID-19 pandemic could have on our business, the continued rapid spread of COVID-19, both across the United States and through much of the world, and the measures taken by the governments of countries and local authorities have disrupted and could delay advancing our product pipeline, delay our and our collaboration partners' clinical trials, delay our overall preclinical activities, and disrupt the manufacture or shipment of both drug substance and finished drug product for our product candidates for preclinical testing and clinical trials and adversely impact our and our collaboration partners' business, financial condition or operating results.

The health and safety of our people and their families continues to be our primary focus. As the COVID-19 pandemic has developed, we have taken numerous steps to help ensure the health and safety of our employees and their families. We are maintaining social distancing and enhanced cleaning protocols and usage of personal protective equipment, where appropriate. Since the stay at home order was put in place in the state of California, the volume of ongoing lab work has been reduced, and only critical program work in the lab has continued with staggered lab employee work shifts to minimize risk of exposure to COVID19, which has and may continue to disrupt or delay our ability to conduct clinical and preclinical research activities. Employees whose tasks can be performed offsite have been instructed to work from home.

We have been actively monitoring our supply chain during the COVID-19 pandemic, including third party materials and service suppliers for us as well as our partners. To date, there have not been any known supply disruptions due to the pandemic, but contingency planning is ongoing with our partners to reduce the possibility of an interruption to manufacturing or the availability of necessary materials.

In April 2020, we announced that the FDA informed Alvogen that additional comparative use human factors data from Forteo experienced users would be necessary for the FDA to make a determination regarding the therapeutic equivalence of the FDA-approved PF708 product relative to Forteo. The COVID-19 pandemic could cause delays in initiating and conducting a comparative use human factors study to generate the additional data requested by the FDA to evaluate the therapeutic equivalence of the FDA-approved PF708 product and Forteo. Our collaboration partners could also experience delays or disruptions that could severely impact their clinical trials and/or preclinical studies. Each of these could adversely affect our and our collaboration partners' ability to obtain regulatory approval for and to commercialize our products and product candidates, increase our operating expenses, and have a material adverse effect on our business and financial results.

COVID-19 has also caused volatility in the global financial markets and threatened a slowdown in the global economy, which may negatively affect our ability to raise additional capital on attractive terms or at all.

We are continuing to assess the potential impact of the COVID-19 pandemic on our business and operations. For additional information on the various risks posed by the COVID-19 pandemic, refer to Part II, Item 1A. Risk Factors of this Quarterly Report on Form 10 Q.

PF708 Comparative Use Human Factors Data

On April 9, 2020, the FDA informed Alvogen that additional comparative use human factors data, specifically from additional Forteo experienced users, would be required before the agency could make a determination about therapeutic equivalence. FDA has indicated that the review of the PF708 therapeutic equivalence package continues and provided guidance on study methodology to generate this additional comparative use human factors data. We plan to work closely with Alvogen and the FDA to generate and submit these additional data as soon as possible. We expect to continue to support Alvogen with its commercial strategy planning in the U.S. while continuing to seek "A" therapeutic equivalence designation.

NT Pharma Deed of Assignment and Amendment

Effective April 21, 2020, we entered into a Deed of Assignment and Amendment (Deed) with NT Pharma, NT International, and Kangchen, a wholly-owned subsidiary of Konruns. Pursuant to the Deed, we agreed to allow NT Pharma to assign its rights and obligations under the NT Pharma Agreement with us to Kangchen. Accordingly, all of NT Pharma's rights under the NT Pharma Agreement will be assigned to Kangchen, and Kangchen will assume all of NT Pharma's obligations under the NT Pharma Agreement. In a related transaction, NT Pharma, through NT International, will obtain an equity interest in Kangchen and each of NT Pharma and Konruns, as the ultimate parents of Kangchen, will jointly and severally guarantee for the benefit of Pfenex the obligations of Kangchen under the NT Pharma Agreement.



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Critical Accounting Policies, Significant Judgments and Use of Estimates

Our management's discussion and analysis of financial condition and results of operations is based on our financial statements, which have been prepared in accordance with accounting principles generally accepted in the United States, or GAAP. The preparation of these financial statements requires us to make estimates and assumptions that affect the reported amounts of assets and liabilities and the disclosure of contingent assets and liabilities at the date of the financial statements, as well as the reported revenue and expenses during the reporting periods. These items are monitored and analyzed by us for changes in facts and circumstances, and material changes in these estimates could occur in the future. We base our estimates on historical experience and on various other factors that we believe are reasonable under the circumstances, the results of which form the basis for making judgments about the carrying value of assets and liabilities that are not readily apparent from other sources. Changes in estimates are reflected in reported results for the period in which they become known. Actual results may differ materially from these estimates under different assumptions or conditions. The accompanying unaudited consolidated financial statements and related financial information should be read in conjunction with the audited financial statements and related footnotes included in our Annual Report on Form 10-K for the year ended December 31, 2019. Except as otherwise disclosed, there have been no material changes in our critical accounting policies and estimates in the preparation of our financial statements during the three months ended March 31, 2020 compared to those disclosed in our Annual Report on Form 10-K for the year ended December 31, 2019, as filed with the SEC on March 11, 2020.

Results of Operations

Comparison of the three months ended March 31, 2020 and 2019

The following table summarizes our net loss during the periods indicated:





                                               Three Months Ended
                                                    March 31,
       (in thousands, except percentages)       2020          2019        Change
       Revenue                               $      682     $  7,862          (91 )%
       Cost of revenue                              340        1,566          (78 )%
       Gross profit                                 342        6,296          (95 )%
       Operating expense
       Research and development                   5,811        7,880          (26 )%
       Selling, general and administrative        4,732        4,543            4 %
       Total operating expense                   10,543       12,423          (15 )%
       Loss from operations                     (10,201 )     (6,127 )         66 %
       Other income, net                             50           69          (27 )%
       Net loss                              $  (10,151 )   $ (6,058 )         68 %




Revenue

Our revenues to date have been generated primarily through collaboration and license agreements. Our collaboration and license agreements frequently contain multiple elements including (i) intellectual property licenses and development services, and (ii) products. Consideration received under these arrangements may include upfront payments, research and development funding, cost reimbursements, milestone payments, payments for product sales and royalty payments. Our customers include Alvogen, NT Pharma, Jazz, Arcellx, and BARDA.





                                               Three Months Ended
                                                    March 31,
        (in thousands, except percentages)     2020           2019        Change
        Revenue                              $    682       $  7,862          (91 )%



Revenue decreased by $7.2 million, or 91%, to $0.7 million in the three-month period ended March 31, 2020, compared to $7.9 million in the same period in 2019. The decrease in revenue was primarily due to significant milestone and upfront payments from Alvogen in the first quarter of last year, attributable to FDA acceptance of our NDA for PF708 and the granting of licenses for additional geographic areas for PF708. In addition, revenue amortization related to our Jazz collaboration agreement was completed in the first half of 2019, work continued to scale back on our Px563L product candidate under our government contract with BARDA, development work on sparX 1 (PF753) and sparX 2 (PF754) for Arcellx was completed, and sales of our CRM197 product decreased. CRM197 revenue will fluctuate depending on stage of development of our customers' and collaboration partners' projects.



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Cost of Revenue



                                               Three Months Ended
                                                    March 31,
        (in thousands, except percentages)     2020           2019        Change
        Cost of revenue                      $    340       $  1,566          (78 )%



Cost of revenue decreased by approximately $1.3 million, or 78%, to $0.3 million in the three month period ended March 31, 2020, compared to $1.6 million in the same period in 2019. The decrease was primarily due to a decrease in sales of our CRM197 product and declining activity related to the BARDA contract.



Research and Development



                                               Three Months Ended
                                                    March 31,
        (in thousands, except percentages)      2020          2019        Change
        Research and development             $    5,811      $ 7,880          (26 )%



Research and development expenses decreased by approximately $2.1 million, or 26%, to $5.8 million in the three month period ended March 31, 2020, compared to $7.9 million in same period in 2019. The decrease in research and development expenses was primarily due to timing of expenses related to our lead product candidate PF708. Significant activity occurred leading up to and shortly after submission of the NDA to the FDA, which occurred in December 2018.

We expect research and development expenses to vary in the near future depending on the phase of the programs we are advancing. The timing and amount of expenses incurred for our product candidates will depend largely upon the outcomes of current or future clinical studies for our product candidates, as well as the related regulatory requirements, manufacturing costs and any costs associated with the advancement of our preclinical programs.

Selling, General and Administrative





                                                Three Months Ended
                                                     March 31,
        (in thousands, except percentages)       2020          2019       Change
        Selling, general and administrative   $    4,732      $ 4,543           4 %



Selling, general and administrative expenses increased by approximately $0.2 million, or 4%, to $4.7 million in the three month period ended March 31, 2020, compared to $4.5 million in the same period in 2019. The increases were primarily due to legal and consulting fees.

Liquidity and Capital Resources

To date, we have funded our operations primarily through the sale and issuance of common stock in our public offerings, revenue from our collaboration agreements, government contracts, service agreements, and reagent protein product sales, our prior credit facility and the private placement of equity securities. At March 31, 2020, we had $65.6 million in cash and cash equivalents and $0.2 million in restricted cash as bank collateral for our corporate credit card program compared to $55.6 million in cash and cash equivalents and $0.2 million in restricted cash as of December 31, 2019.

In July 2016, we entered into a development and license agreement with Jazz Pharmaceuticals for the development and commercialization of multiple early stage hematologic oncology product candidates, including PF743 (JZP-458), a recombinant Erwinia asparaginase, and PF745 (JZP-341), a long-acting Erwinia asparaginase, and in the third quarter of 2017, achieved a process development milestone. The agreement also includes an option for Jazz to negotiate a license for a recombinant pegaspargase product candidate with us. Under the terms of the agreement, we received an upfront and option payment totaling $15.0 million in July 2016 and may be eligible to receive additional payments based on the achievement of certain research and development, regulatory, and sales-related milestones.



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In December 2017, we and Jazz entered into an amended and restated agreement, bringing the total value of payments and potential payments associated with the collaboration to $224.5 million. In addition, we may be eligible to receive tiered royalties on worldwide sales of any products resulting from the collaboration at rates reduced from those under the 2016 agreement. Under the amended and restated agreement, in the second quarter of 2018, we achieved two process development milestones for PF745. In September and December 2019, we achieved development milestones and recognized $11.0 million and $15 million in revenue for successful achievement of process development milestones for PF745, and we received cash payment for these milestones in the fourth quarter of 2019.

In October 2019, the FDA approved the NDA for PF708 submitted under the 505(b)(2) regulatory pathway, with Forteo® (teriparatide injection) as the reference drug. We expect to continue to support Alvogen, our collaboration partner, with its commercial strategy planning in the U.S. while continuing to seek "A" therapeutic equivalence designation. In consideration for the licenses and other rights granted to Alvogen under the agreement, we received an upfront payment of $2.5 million, and to date have achieved two development milestones for $2.5 million each, one of which was the milestone achievement for FDA approval of PF708 in October 2019, and may be eligible to receive up to $15 million in support and regulatory milestone payments, which amount is subject to reductions over time. We are also eligible to receive a 50% gross profit split on sales if the product is rated as Therapeutically Equivalent (TE) to Forteo and up to 40% if rated differently.

In March 2018, we entered into an equity sales agreement (2018 Sales Agreement) with William Blair to sell shares of our common stock having aggregate sales proceeds of up to $20.0 million, from time to time, through an ATM equity offering program under which William Blair would act as sales agent. Under the 2018 Sales Agreement, we set the parameters for the sale of shares, including the number of shares to be issued, the time period during which sales are requested to be made, limitation on the number of shares to be issued, the time period during which sales are requested to be made, limitation on the number of shares that may be sold in any one trading day and any minimum price below which sales may not be made. The 2018 Sales Agreement provided that William Blair would be entitled to compensation for its services equal to 3.0% of the gross sales price per share of all shares sold through William Blair under the Sales Agreement. In January and February 2020, we sold a total of 1.8 million shares of our common stock through the "at-the-market" equity offering program for aggregate gross proceeds of approximately $20.0 million, at which point the Sales Agreement automatically terminated.

On May 25, 2018, we closed an underwritten public offering of 7,820,000 shares of our common stock at a price of $5.50 per share, which included the full exercise by the underwriters of their option to purchase an additional 1,020,000 shares of our common stock. Net proceeds from this offering were approximately $39.5 million.

In May 2020, we entered into an equity sales agreement (2020 Sales Agreement) with William Blair and Wainwright to sell shares of our common stock having aggregate sales proceeds of up to $60.0 million, from time to time, through an ATM equity offering program under which William Blair and Wainwright will act as sales agents. As of May 7, 2020, we had not sold any shares under this 2020 Sales Agreement.

We believe that our existing cash and cash equivalents and our cash inflow from operations will be sufficient to meet our anticipated cash needs for at least the next 12 months. We have based this estimate on assumptions that may prove to be wrong, and we could utilize our available capital resources sooner than we currently expect. Further, our operating plan may change, and we may need additional funds to meet operational needs and capital requirements for product development and commercialization sooner than planned. We currently have no credit facility or committed sources of capital although we may receive milestone and other contingent payments under our current license and collaboration agreements. Because of the numerous risks and uncertainties associated with the development and commercialization of our product candidates and the extent to which we may enter into additional agreements with third parties to participate in their development and commercialization, we are unable to estimate the amounts of increased capital outlays and operating expenditures associated with our current and anticipated clinical trials. Our future capital requirements will depend on many factors, including:



  • the timing and extent of spending on our research and development efforts;


    •   our ability to enter into and maintain collaboration, licensing,
        commercialization and other arrangements and the terms and timing of such
        arrangements;


    •   our ability to retain Alvogen as a collaboration partner for the
        FDA-approved PF708 product and PF708 on commercially acceptable terms;


    •   the timing of the marketing authorization for PF708, if any, in
        jurisdictions outside the United States;


    •   whether we and Alvogen obtain, in a timely manner or at all, an "A"
        therapeutic equivalence designation for the FDA-approved PF708 product
        that may allow such product to be automatically substituted for Forteo
        depending on applicable laws and policies within each of the 50 states;


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    •   the cost to us of development, manufacturing and commercialization
        activities for PF708 and our other product candidates, if any;


    •   the cost of preparing, filing, prosecuting, defending and enforcing any
        patent claims and other intellectual property rights;


  • the receipt of any collaboration or milestone payments;


    •   the scope, rate of progress, results and FDA acceptance of the results,
        and cost of our clinical trials, preclinical testing and other related
        activities for our product candidates;


  • the emergence of competing technologies or other adverse market developments;


    •   the time and costs involved in seeking and obtaining regulatory and
        marketing approvals in multiple jurisdictions for our product candidates
        that successfully complete clinical trials;


    •   the introduction of new product candidates and the number and
        characteristics of product candidates that we pursue;


    •   the timing, receipt and amount of sales, profit sharing or royalties, if
        any, from the FDA-approved PF708 product, PF708, and any other potential
        products;


    •   the degree and rate of market acceptance and coverage and reimbursement by
        payors of the FDA-approved PF708 product, PF708 and any of our other
        product candidates launched by us or our collaboration partners; the
        impact of any natural disasters or public health crises, such as the
        COVID-19 pandemic;


  • the potential expansion of our sales and marketing activities; and


    •   the potential acquisition and in-licensing of other technologies, products
        or assets.

If we were to experience any delays or encounter issues with any of the above, including with respect to obtaining an "A" therapeutic equivalence designation for the FDA-approved PF708 product, Alvogen's commercial launch of the FDA-approved PF708 product in the U.S., clinical holds, failed studies, inconclusive or hard-to-interpret results, safety or efficacy issues, or other regulatory challenges that require longer follow-up of existing studies, additional major studies, or additional supportive studies in order to pursue marketing approval, it could further increase the costs associated with the above and delay or suspend revenues.

We may need to raise additional capital to fund our operations in the near future. Funding may not be available to us on acceptable terms, or at all and our ability to raise additional capital may be adversely impacted by potential worsening global economic conditions and the recent disruptions to and volatility in the credit and financial markets in the United States and worldwide resulting from the COVID-19 pandemic. If we are unable to obtain adequate financing when needed, we may have to delay, reduce the scope of or suspend one or more of our clinical trials, research and development programs or commercialization efforts. We may seek to raise any necessary additional capital through a combination of public or private equity offerings, debt financings, collaborations, strategic alliances, licensing arrangements and other marketing and distribution arrangements. To the extent that we raise additional capital through marketing and distribution arrangements or other collaborations, strategic alliances or licensing arrangements with third parties, we may have to relinquish valuable rights to our product candidates, future revenue streams, research programs or product candidates or to grant licenses on terms that may not be favorable to us. If we do raise additional capital through public or private equity offerings, the ownership interest of our existing stockholders will be diluted, and the terms of these securities may include liquidation or other preferences that adversely affect our stockholders' rights. If we raise additional capital through debt financing, we may be subject to covenants limiting or restricting our ability to take specific actions, such as incurring additional debt, making capital expenditures or declaring dividends.

Cash Flows

The following table sets forth the primary sources and uses of cash, cash equivalents and restricted cash for each of the periods presented below:





                                                              Three Months Ended
                                                                  March 31,
(in thousands)                                              2020              2019
Net cash (used in) provided by:
Operating activities                                    $      (8,656 )   $    (10,338 )
Investing activities                                           (1,433 )           (111 )
Financing activities                                           20,067              (17 )
Net increase (decrease) in cash, cash equivalents and
restricted
  cash                                                  $       9,978     $    (10,466 )


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Net cash used in operating activities

Net cash used in operating activities was $8.7 million during the three months ended March 31, 2020 compared to $10.3 million during the same period in 2019. The decrease in net cash used in operating activities was primarily due to a decrease in the amounts owed by BARDA, Alvogen and several other collaboration partners and customers, partially offset by an increase in net loss in the three months ended March 31, 2020 compared to the same period in 2019.

Net cash used in investing activities

Net cash used in investing activities was $1.4 million during the three months ended March 31, 2020 compared to $0.1 million used in the same period in 2019. The increase in cash used in investing activities was primary due to the purchase of additional property and equipment in the three months ended March 31, 2020.

Net cash provided by financing activities

Cash provided by financing activities was $20.1 million during the three months ended March 31, 2020 compared to cash used in financing activities of $17 thousand during the same period in 2019. In January 2020, we sold 500,000 shares for net proceeds of $6.2 million, and in February 2020, we sold an additional 1,253,443 shares for net proceeds of $13.2 million.

Off-Balance Sheet Arrangements

In the normal course of business, we enter into contracts and agreements that contain a variety of representations and warranties and provide for general indemnifications. Our exposure under these agreements is unknown because it involves claims that may be made against us in the future but have not yet been made. As of March 31, 2020, we have not paid any claims or been required to defend any action related to our indemnification obligations. However, we may record charges in the future as a result of these indemnification obligations.

Contractual Obligations and Commitments

There have been no material changes during the three months ended March 31, 2020 to our contractual obligations disclosed in our "Management's Discussion and Analysis of Financial Condition and Results of Operations" included in our Annual Report on Form 10-K for the year ended December 31, 2019.

Recently Adopted Accounting Pronouncements

In August 2018, the FASB issued ASU No. 2018-15, Intangibles-Goodwill and Other-Internal-Use Software (Subtopic 350-40): Customer's Accounting for Implementation Costs Incurred in a Cloud Computing Arrangement That Is a Service Contract. This new guidance aligns the requirements for capitalizing implementation costs incurred in a hosting arrangement that is a service contract with the requirements for capitalizing implementation costs incurred to develop or obtain internal-use software. ASU 2018-15 is effective for us beginning in the first quarter of fiscal year 2020, with early adoption permitted. We have adopted this standard as of January 1, 2020 using the prospective method. The impact of adopting this standard to our consolidated financial statements was immaterial.



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